About this Author

College chemistry, 1983

The 2002 Model

After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: derekb.lowe@gmail.com
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June 26, 2005

How Not to Do It: Vacuum Pumps

Posted by Derek

I wandered into the lab one Saturday morning while I was in graduate school - (OK, scratch that, I wandered into the lab most Saturday mornings while I was in graduate school, which was one of the things I hated about it.) And as I walked past the vacuum pump, I noticed something a little odd.

For those who don't work in a synthetic chemistry lab, the vacuum pump is where you put flasks of stuff after you've evaporated most of the solvent off of them. The pump pulls the last volatiles residues out of your syrup, crystals, or powder, leaving you with a dry weight that you can use to check your reaction yield, get pure spectra of the material, and so on.

The pump was making a different sound than usual. There was more of a rattle in it this morning, and less of a hum, if that makes any sense. I looked the thing over, trying to see what was going on, and finally I checked the row of stopcocks. Pay dirt! One of them was wide open, and the reason the pump was making that unusual sound was that it was trying to pump the air out of the entire chemistry building.

That isn't good for them. And in an academic lab, it's not like you could just reach into a cabinet and pull out another vacuum pump when you burned one out. They aren't cheap, and we spent time fixing the ones we had rather than attempt to ever buy new ones. So I twisted the glass stopcock closed, muttering foul gerunds, and left an unpleasant note taped to it. Something about how if you were the last user of this pump, you left the procreating stopcock open, and you shouldn't reproducing do that, etc. And I went about the rest of my merry morning's work.

The next morning, I wandered into the lab yet again. (I was there most Sunday mornings, too, damn it all.) And as I walked past the pump, I could swear that something was odd yet again. Surely not. I went back, looked it over, but couldn't see anything out of whack. Then, hardly believing it, I moved my taped note back to find the same stopcock, left wide open again. The slackjaw that did it it had to hold the note up to get to the stopcock, which really defied belief. There was the poor vacuum pump, trying to evacuate the air out of the state of North Carolina again.

I went stomping through our labs, looking for the culprit. But I was the only person there. No one in my group had done anything like that, so I wondered if someone else had been in there. . .then I remembered a Moroccan biochemist from another group who came over sometimes to hang out with the guy around the corner from me. Maybe. . .I went over to the next hall, and there was the pride of Marrakesh himself, humming tunelessly as he wandered about his lab.

So in I went, demanding to know if he'd been in our lab that morning, used our vacuum pump, and so on. He gave me a big grin: "No, I have not used this pump. But I have gone past it this morning, and I have thought, Hmmm, she is sucking ze air, no?" My testy reply was that if I found out that he'd been leaving the pump open then he would be sucking ze air, yes. For whatever reason, our apparatus went unmolested after that.

Back when one performed Southern blots in a Tupperware container in a shaking water bath (at least I'm too young to have used Seal-A-Meal bags!), an idiot grad student in my lab loved to fill the bath to the brim and run it at maximum speed, because a) he thought the sloshing was amusing and b) he had a general notion that setting things higher made him somehow "better".

He burned the thing out every six weeks or so, putting us all out of action for a week every time. The PI was too afraid of his tantrums to tell him to stop, so eventually we just bought a second shaker bath.

Actually, letting a pump draw air - for a brief period! - improves the vacuum it will pull because the air rapidly purges organic vapors dissolved in the oil (which otherwise will outgas slowly under vacuum). (Rather like sparging solvents with He.)

Not really relevant for mere solvent removal, whcih doesn't require much of a vacuum, but critical for pulling a hard vacuum.

I've heard that about running air through the pump, but I've never needed to worry about that low a pressure. Doubtless that's what my Moroccan guy was trying to do, help us out. (!) But Drew's right, the vacuum trap is a real problem. We used dry ice, not liquid nitrogen, though, so we were in better shape in that regard.

For non-chemists, you put a cold trap between your vacuum lines and the pump to keep solvent vapors and the like out of the pump oil. The colder, the better, so liquid nitrogen works really well. But that's cold enough to condense oxygen out of the air if you let it, which can be Bad News if it starts to pile up on flammable solvents - even when it's that cold.

I wasn't thinking about that problem at the time; I just wanted to pound whoever it was that was silly enough to walk away from an open vacuum stopcock.

Some vacuum pumps have a "gas ballast valve" that deliberately lets a little air in while the pump is running, for the reason SRC mentioned (purging organic vapors).

This proved to be a useful piece of knowledge when the !@#%^&* undersized LN2 trap filled up with condensate and inhaled a non-negligible quantity of methylene chloride + acetic acid. That was very fun. (And yes, the pump did survive and go on to an undistinguished career evacuating the Roto-Vap. But it was a near-run thing.)